The 2017 Workshop on Phylogenomics will be held in Český Krumlov, Czech Republic, from 22 January – 4 February. This will be the first version of the Workshop on Phylogenomics, which extends on topics developed in both the  Workshop on Molecular Evolution and the Workshop on Genomics placing them in a phylogenomic framework.

More information

This workshop brings together an international collection of faculty members and Workshop participants to study and discuss current ideas and techniques for exploring phylogenomics. The Workshop consists of a series of lectures, demonstrations and computer laboratories that cover theoretical and conceptual aspects of large-scale phylogenetics and phylogenomics, with a strong emphasis on data analysis.

The Workshop places a strong focus on molecular phylogenetics performed at genome-wide scales (phylogenomics), and covers all aspects of phylogenomics workflows. The workshop will cover main aspects of phylogenomics: the reconstruction of species trees from large-scale genomics data. In addition, we will explore the use of phylogenomic data to 1) study species divergence and trait evolution patterns, 2) reconstruct and analyze genome-wide collections of species trees to detect orthology and paralogy, and 3) study genome dynamics along species trees.

A majority of the schedule is dedicated to hands-on learning activities designed by faculty and the workshop team. This interactive experience provides Workshop participants with the practical experience required to meet the challenges presented by modern evolutionary sciences.

The Workshop registration fee is $1,800. This amount does not cover travel, lodging or boarding. Many important details about this and other topics can be read on our FAQ page and a map of important locations: Workshop Guide.

Detailed information about housing and discounted rates can be viewed here.

A full schedule can be viewed below. Modifications and additions to the schedule may be made at any time prior to the beginning of the Workshop; however, the overall content and structure will remain largely the same.

The Workshop on Genomics is organized and Co-directed by:

Toni Gabaldon, Center for Genomic Regulation (CRG), Barcelona

Jordi Paps Montserrat, University of Essex, UK

Guy Leonard, University of Exeter, UK

Scott Handley, Washington University School of Medicine, St. Louis, USA



T-Shirt Competiton

Public DNS

Tree Competition


Week 1: 22-28 January, 2017

Date Time Presenter Topic Location
22 Jan 6p – 10p Everyone Reception Hotel Zlatý Anděl
23 Jan 9a – 12p Scott Handley & Toni Gabaldón Introduction and Orientation | Town Options and Information Minorite Monastery
2p – 5p Guy Leonard & Jordi Paps Introduction to the Laboratory and UNIX (short and advanced tutorials) Study Centre
7p – 10p Workshop Participants

Toni Gabaldón & Marina Marcet-Houben

Scientific Speed Networking

Python (IntroCMBI tutorial & UWaterloo tutorial) & ETE3 (tutorial)

Study Centre
24 Jan 9a – 12p  Toni Gabaldón Introduction to Phylogenetic Inference Monastery
2p – 5p Toni Gabaldón Orthology and Paralogy Monastery
7p – 10p Toni Gabaldón Orthology and Paralogy Detection Lab (test dataset & cont.) + Python/ETE3 (cont.) Study Centre
25 Jan 9a – 12p Antonis Rokas  Introduction to Phylogenomics Monastery
2p – 5p Workshop Instructors (Lisa & Marina) Alignment (PASTA) and Alignment Trimming (trimal and test datasetLab Study Centre
7p – 10p Workshop Instructors (Rosa) Alignment Concatenation (phyutility) Lab Study Centre
26 Jan 9a – 12p Xiaofan Zhou Fast Phylogenetic Approaches Monastery
2p – 5p Xiaofan Zhou Maximum Likelihood LabRAxML Study Centre
7p – 10p Workshop Instructors Maximum Likelihood LabPhyMLIQ-TREE & FastTree (FastTree challenge & ML challenge) Study Centre
27 Jan 9a – 12p Tracy Heath Bayesian Phylogenetic Inference Monastery
2p – 5p Tracy Heath Bayesian Phylogenetic Inference Lab Study Centre
7p – 10p Tracy Heath Divergence Time Estimation (WH Intro & Lab) Study Centre
28 Jan 9a – 12p David Swofford Hypothesis Testing in Phylogenetics (jModelTest2PAUP*, and PartitionFinder2) Study Centre
2p – 5p David Swofford Model Selection Lab (model selection simulation tutorialmorning dataset, and afternoon dataset) Study Centre
6p – 10p Everyone Workshop Social Event: 6p city tour (meet at Náměstí Svornosti) and 7p dinner at Hostinec Depo Hostinec Depo

Week 2: 29 January – 4 February, 2017

Date Time Presenter Topic Location
29 Jan All Day Everyone Free Day Anywhere
30 Jan 9a – 12p Joe Bielawski Detecting Selection (Parts 1 and 2 & 3) Monastery
2p – 5p Joe Bielawski Detecting Selection Lab (PAML Basic and Advanced Tutorials) Study Centre
7p – 10p Workshop Instructors (Rosa & Marina) Techniques for Generating Phylogenomic Data MatricesTranscriptomics vs. Genomics Study Centre
31 Jan 9a – 12p Laura Kubatko Species Tree Estimation Monastery
2p – 5p Laura Kubatko SVDquartets Lab (Intro & tutorial + gene tree distribution demo) Study Centre
7p – 10p Workshop Instructors (Lisa & Miguel) Tree Editing and Visualization / Open Lab Study Centre
1 Feb 9a – 12p Matthew Hahn Analysis of Gene Gain and Loss (Parts 1, 2 and 3) Monastery
2p – 5p Matthew Hahn CAFE Lab (tutorial – updated) Study Centre
7p – 10p Matthew Hahn CAFE Lab cont. / Open Lab Study Centre
2 Feb 9a – 12p Céline Scornavacca Non-Vertical Evolution and Phylogenetic Networks (Intro & Methods) Monastery
2p – 5p Céline Scornavacca Non-Vertical Evolution Lab (datapractical) Study Centre
7p – 10p Workshop Instructors Open Lab Study Centre
3 Feb 9a – 12p Jordi Paps Montserrat | Everyone LBA & Animal Nightmares | Open Lab Study Centre
2p – 5p Jordi Paps Montserrat | Everyone Downloading your data | Final Open Lab Study Centre
7p – 10p Everyone End of Workshop Dinner (6p) and Party Hostinec Depo
4 Feb All Day Everyone Departure